BUENOS AIRES — One Argentine priest is on trial in Tucumán Province on charges of working closely with torturers in a secret jail during the so-called Dirty War, urging prisoners to hand over information. Another priest was accused of taking a newborn from his mother, one of the many baby thefts from female prisoners who were “disappeared” into a system of clandestine prisons.

Another clergy member offered biblical justification for the military’s death flights, according to an account by one of the pilots anguished about dumping drugged prisoners out of aircraft and into the sea.

As he starts his papacy, Francis, until this month Jorge Mario Bergoglio, the archbishop of Buenos Aires, faces his own entanglement with the Dirty War, which unfolded from 1976 to 1983. As the leader of Argentina’s Jesuits for part of that time, he has repeatedly had to dispute claims that he allowed the kidnapping of two priests in his order in 1976, accusations the Vatican is calling a defamation campaign.

Now his election as pope is focusing scrutiny on his role as the most prominent leader of the Roman Catholic Church in Argentina, an institution that remains under withering criticism for its role in failing to publicly resist — and in various instances actively supporting — the military dictatorship during a period when as many as 30,000 people are thought to have been killed or disappeared.

This stance by Argentina’s church stands in contrast to the resistance against dictatorships by Catholic leaders elsewhere in Latin America at the time — notably in Chile and Brazil, two nations where far fewer people were killed. Even as the head of the Argentine Conference of Bishops from 2005 to 2011, Francis resisted issuing a formal apology for the church’s actions during the Dirty War, disappointing human rights campaigners.

“The combination of action and inaction by the church was instrumental in enabling the mass atrocities committed by the junta,” said Federico Finchelstein, an Argentine historian at the New School for Social Research in New York. “Those like Francis that remained in silence during the repression also played by default a central role,” he said. “It was this combination of endorsement and either strategic or willful indifference that created the proper conditions for the state killings.”

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The church rejected claims by Jorge Videla, third from right, ex-head of the junta, on the role that bishops played.Credit
Enrique Marcarian/Reuters

Francis, 76, has offered a complex description of his role during the dictatorship, a period officially called the Process of National Reorganization, in which the authorities installed a terrifying campaign against perceived opponents.

While refraining from public criticism of the dictatorship, Francis said in his autobiography that he pressed military officials behind the scenes to free the two priests from his order — Orlando Yorio and Francisco Jalics — even meeting with top military officials.

Francis also said that he hid at a Jesuit school several people persecuted by the dictatorship, and even helped one young man who resembled him to flee Argentina, via Foz do Iguaçu on the Brazilian border, giving him priest’s garb and his own identity documents.

The Rev. Ignacio Pérez del Viso, a Jesuit who is a longtime friend of Francis’, said that a small number of Argentine bishops spoke out against the military dictatorship. But they were clearly in the minority, he said, and others in the Argentine church, including the new pope, who was 39 at the time of the 1976 coup, adopted a far more cautious position.

“When you saw that the majority of the bishops preferred to have a dialogue with the military,” Father Pérez del Viso, 78, said, “it’s not easy to say, ‘We will do something different.’ ” He added: “Many of the bishops opted, rather than to confront the military head on, to try to intercede in private conversations for those they could save.”

“Later the bishops realized this was a mistake,” Father Pérez del Viso said. “But to see the mistake at that moment was difficult.”

Religious scholars attribute such passivity to remarkably close ideological and political links between the church and the armed forces. Some priests have even been forced to stand trial on charges of human rights abuses.

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The Rev. Christian von Wernich, a former police chaplain, was convicted of complicity in the killing of political prisoners.Credit
El Dia

After a previous military coup in Argentina in 1930, the church forged a role as a spiritual guide for the armed forces. By the time military rule was established again in the 1970s, their operations overlapped to the point where some bishops were provided soldiers as personal servants in their palaces, and only a handful of bishops publicly condemned the dictatorship’s repression.

“Of all the national churches in Latin America, Argentina is where ties were closest between the clergy and the military,” said Kenneth P. Serbin, a historian at the University of San Diego.

This legacy presents a challenge to Francis. Last week, a judge who took part in an investigation into a clandestine prison at the Naval Mechanics School said the inquiry uncovered no evidence that Francis was involved in the kidnapping of the Jesuits. “It is totally false to say that Jorge Bergoglio handed over those priests,” the judge, Germán Castelli, was quoted as saying in the newspaper La Nación.

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But doubts persist, based on the priests’ own accounts, including a 1977 report by Father Yorio to the Jesuit authorities, obtained by The New York Times, and a 1994 book by Father Jalics.

Father Yorio wrote that Francis, who was then the top Jesuit in Argentina, told them he supported their work even as he sought to undermine it, making negative reports about them to local bishops and claiming they were in the slum without his permission.

“He did nothing to defend us, and we began to question his honesty,” wrote Father Yorio, who died in 2000. Finally, without telling the two priests, Father Yorio wrote, Francis expelled them from the Jesuit order.

Three days later, hundreds of armed men descended on the slum and seized the two priests. Father Yorio was interrogated and accused of being a guerrilla. The priests were kept for five months, chained hand and foot and blindfolded, fearing they would be killed.

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Finally, they were dropped off in a drugged state on the outskirts of Buenos Aires.

In a statement posted on a Jesuit Web site last week, Father Jalics said he would not comment “on the role of Father Bergoglio in these events.” He said that years after the kidnapping, they celebrated a Mass together and he solemnly embraced him. “I am reconciled to the events and view them from my side as concluded,” Father Jalics wrote.

But in an interview, Father Yorio’s sister, Graciela Yorio, accused Francis of leaving the priests “totally unprotected” and making them an easy target for the military. She said that her brother and Father Jalics, whom she referred to using his name in Spanish, were in agreement about Francis’ role. “My brother was certain,” she said, “And Francisco, too, Francisco Jalics. I have no reason not to believe my brother’s word.”

Still, several prominent leftists here have defended Francis, emphasizing his openness to dialogue and austere habits. “He is questioned for not having done all he could do,” said Adolfo Pérez Esquivel, a pacifist and winner of the Nobel Peace Prize. “But he was never an ally of the dictatorship.”

Though Francis has had to respond to doubts about his own past during the Dirty War, he has faced other issues that still haunt the church. He was head of Argentina’s bishops’ conference in 2007, when the Rev. Christian von Wernich, a former police chaplain, was found guilty of complicity in the killing and torture of political prisoners.

Even after his conviction, Father von Wernich was allowed to offer Mass to fellow prison inmates. Other priests have similarly faced charges related to abuses from the dictatorship era. And still there are other priests who have not been charged with a crime, but who face serious accusations about their connection to the armed forces.

The church has tried to account on different occasions for its actions during the dictatorship. In 2000, it apologized for its “silences” that enabled rights abuses. And last November, after the future pope’s tenure as head of the bishops’ conference had ended, the church issued another statement in response to the assertion by Jorge Videla, the former head of the military junta, that Argentine bishops had in effect collaborated with the dictatorship.

The church rejected Mr. Videla’s claim, but said it would “promote a more complete study” of the Dirty War years.

A version of this article appears in print on March 18, 2013, on Page A1 of the New York edition with the headline: Starting a Papacy, Amid Echoes of a ‘Dirty War’. Order Reprints|Today's Paper|Subscribe